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Topic: Visual molecular dynamics

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	Title of Your Paper
		To understand and interpret the molecular dynamics results and to come up with new hypotheses the user often needs visualization and querying tools to be interactively involved in the process of visual data mining and querying of the spatio-temporal data.
		Molecular visualization and analysis systems use advantages of computer graphics, data mining, virtual reality, and even cognitive psychology to provide biologists with a deep insight into complex structures, fine features, and obscure patterns in large-scale datasets.
		System gOpenMol is a tool for visualization and analysis of molecular structures combined with several applications for data analysis and presentation originated from quantum mechanics, molecular dynamics and other computational chemistry calculations.
	www.cgg-journal.com /example (2516 words)

	Visual Molecular Dynamics - Wikipedia, the free encyclopedia
		VMD is primarily developed as a tool for viewing and analyzing the results of molecular dynamics simulations, but it also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects.
		VMD has been developed by the Theoretical and Computational Biophysics group at the University of Illinois and the Beckman Institute.
		The initial version of VMD was written by Andrew Dalke, Jeff Ulrich, and William Humphrey and was released in 1995.
	en.wikipedia.org /wiki/Visual_molecular_dynamics (335 words)

	Advanced Biomedical Computing Center:VMD infomation
		VMD is a molecular visualization program for displaying and animating large biomolecular systems using 3-D graphics.
		VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
		VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.
	www.abcc.ncifcrf.gov /app/htdocs/appdb/appinfo.php?appname=VMD (193 words)

	TREMOLO - parallel molecular dynamics
		TREMOLO is the name of the combined molecular dynamics software packages treemol and molgrid, using both tree algorithms for long-ranged potentials as well as grid algorithms for short- and long-ranged potentials.
		Molecular dynamics simulations of the elastic moduli of polymer-carbon nanotube composites.
		Molecular simulation of the influence of chemical cross-links on the shear strength of carbon nanotube - polymer interfaces.
	wissrech.iam.uni-bonn.de /research/projects/tremolo (305 words)

	Computer Graphics World - Molecular Vision
		Called VMD (Visual Molecular Dynamics), the tool was initially developed by TBG students as the visualization front-end to the group`s MDScope software--an integrated environment of computational tools for the simulation and study of biopolymers.
		VMD can also act as a graphical front end for an external molecular dynamics program by displaying and animating a molecule undergoing simulation on a remote computer.
		From its conception, VMD was working with solid representations." In fact, says Stone, the first version of the software--a tool called VRChem developed by then graduate student Bill Humphrey--was one of the earliest forays into the use of 3D and hardware-accelerated graphics in molecular visualization with solid representations.
	cgw.pennnet.com /Articles/Article_Display.cfm?Section=Archives&Subsection=Display&ARTICLE_ID=50426&KEYWORD=vmd (945 words)

	Molecular Visualization
		VMD is a versatile, modifiable, fully documented molecular visualization program, and is freely distributed.
		VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bylayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.
		VMD is copyrighted by the Theoretical Biophysics Group and the Board of Trustees of the University of Illinois.
	www.mayo.edu /bir/Projects/MoleculeVis/MolecularVis.html (377 words)

	VMD - Visual Molecular Dynamics
		VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
		VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
		This lighting used in concert with traditional point source lights and directional lights to increase the perception of shape and depth in images of molecular structures, and decreases the deleterious effects of harsh shadows which otherwise occur with lighting based on a small number of direct light sources.
	www.ks.uiuc.edu /Research/vmd (307 words)

	The Amber Molecular Dynamics Package (Site not responding. Last check: 2007-10-28)
		"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
		Molecular dynamics simulation of nucleic acids: Successes, limitations and promise.
		H++ is a tool to estimate pKa's of protein side chains, and to automate the process of assigning protonation states for molecular dynamics simulations.
	amber.scripps.edu (2557 words)

	Molecular Modeling Programs
		VMD (Visual Molecular Dynamics): VMD " is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.
		In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer." We will use this program to display the results of molecular dynamics calculations using NAM, which is described below.
		NAMD (Scalable Molecular Dyanics): NAMD is a molecular dynamics code that can be run on the Beowulf parallel PC cluster in the computer science department.
	employees.csbsju.edu /hjakubowski/classes/ch331/bcintro/molecularmodelingprograms.htm (570 words)

	Research Computing Technologies
		The Visual Molecular Dynamics (VMD) program is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
		VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, and others.
		In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
	www.ats.ucla.edu /rct/software/chemistry/vmd.htm (182 words)

	MPG \| VMD: Visual Molecular Dynamics
		Application for molecular visualization; lets you display, animate and analyze large biomolecular systems; includes source code.
		VMD uses OpenGL for 3-D rendering of molecules.
		VMD can animate molecular dynamics simulation trajectories, and perform scripted analysis functions with its built-in Tcl scripting component.
	guide.apple.com /action.lasso?-database=macosguide&-layout=cgi_detail&-response=/ussearch/detail.html&prodkey=47756&-search (132 words)

	Molecular Animation: VMD (Site not responding. Last check: 2007-10-28)
		VMD (Visual Molecular Dynamics) is a freely available molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
		VMD has excellent documentation which is available online.
		The VMD home page has a Script Library which users may download and modify to suit their needs.
	www.msi.umn.edu /bscl/tutorials/molanim/vmd (244 words)

	Molecular Dynamics Investigation of Primary Photoinduced Events in the Activation of Rhodopsin -- Saam et al. 83 (6): ...
		Molecular Dynamics Investigation of Primary Photoinduced Events in the Activation of Rhodopsin -- Saam et al.
		A new photolysis intermediate in artificial and native visual pigments.
		Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin.
	www.biophysj.org /cgi/content/full/83/6/3097 (8004 words)

	People - MICE
		In contrast to MICE, which is designed provide simple visualization capabilities in a collaborative setting, the MidasPlus package is the basis for work on a new tool that will enable full blown molecular modelling on a collaborative basis.
		VMD (Visual Molecular Dynamics) is a molecular visualization program from the Theoretical Biophysics group of the University of Illinois.
		Spock is another general purpose molecular visualization program, but it also includes Internet conferencing facilities that allow a view to be shared between multiple users on a network.
	mice.sdsc.edu /site/people.html (633 words)

	Molecular Docking Tools from Garrett M. Morris' Home Page (Site not responding. Last check: 2007-10-28)
		MMDB: The Molecular Modeling Database - from NCBI, this is a compilation of all the Brookhaven Protein DataBank 3-dimensional structures of biomolecules from crystallographic and NMR studies.
		Moviemol is a program for visualization and animation of molecular structures for PC's, IBM RS/6000 and SGI workstations.
		VMD - Visual Molecular Dynamics from the Theoretical Biophysics Group at the University of Illinois at Urbana-Champaign.
	www.scripps.edu /mb/olson/doc (1815 words)

	[No title] (Site not responding. Last check: 2007-10-28)
		vmd@ks.uiuc.edu VMD is a molecular graphics program designed for the interactive visualization of bioppolymers such as proteins, nucleic acids, and lipids and membranes.
		Visualization of dynamics molecular data - VMD can read and animate DCD files or acquire the timestep information from a running molecular dynamics program.
		VMD uses the Tcl script language which allows for the creation of loops, functions, and other control structures as well as being extensible in its own right.
	www.netlib.org /utk/misc/sw_survey/urc/VMD.urc (419 words)

	origin Software: Category: Molecular Simulation (Site not responding. Last check: 2007-10-28)
		Molecular simulation programs used to study the dynamic and thermodynamic behavior of molecular system.
		Equilibrium properties, such as radial distribution functions and free energies, and dynamical properties, such as diffusion constants, are be computed by solving Newton's equation with forces derived from an empirical force field.
		NAMD is a molecular dynamics code designed for high-performance simulation of large biomolecular systems.
	www.msi.umn.edu /origin/software/MolecularSimulation.html (235 words)

	Apple - Downloads - Math & Science - VMD - Visual Molecular Dynamics 1.8.1 (Site not responding. Last check: 2007-10-28)
		VMD loads many molecular structure file formats, electron density map formats, and graphics files using a plugin-based file reader system.
		VMD includes built-in movie making features and supports a variety of external ray tracing programs.
		VMD also includes extensions for viewing sequence data and for performing interactive molecular dynamics simulations with haptic feedback.
	www.apple.com /downloads/macosx/math_science/vmdvisualmoleculardynamics.html (164 words)

	BONUS MS ENCARTA ENCYCLOPEDIA DELUX 2004 (Site not responding. Last check: 2007-10-28)
		VMD provides visualization, analysis, and Tcl/Python scripting features, and has recently added sequence browsing and volumetric rendering features.
		Unfortunately, these Brave New Strategies, things like.NET and Longhorn and Avalon, trying to create a new API to lock people into, can't work very well if everybody is still using their good-enough computers from 1998.
		A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems Coriander - Coriander is a 1394 camera controller for Linux.
	www.bonus-ms-encarta-encyclopedia-delux-2004.247softwareshop.net (7333 words)

	National Partnership for Advanced Computational Infrastructure: Archives
		Schulten's talk concerned the constellation of techniques developed in his lab, in particular Steered Molecular Dynamics (SMD), and their use in explaining the mechanics of biopolymers and finding the underlying unbinding potentials (the amount of force needed to "unfold" a protein, for example).
		The force constants used in the dynamics simulation are similar to those used in atomic force microscopy (AFM), which permits actual physical manipulation of the molecular complex.
		To examine in atomic detail the dynamics and structure-function relationships of this behavior, SMD simulations of force-induced titin Ig domain unfolding were performed by the group of Klaus Schulten at the University of Illinois.
	www.npaci.edu /online/v4.13/schulten.html (1129 words)

	VMD - Visual Molecular Dynamics (Site not responding. Last check: 2007-10-28)
		VMD is a molecular graphics program designed for the interactive
		visualization of bioppolymers such as proteins, nucleic acids,
		VMD is the visualization component of the MDScope project
	www.netlib.org /utk/misc/sw_survey/urc/html/VMD.1.html (278 words)

	Dimension Technologies Inc. - VMD Now Supports DTI Displays
		VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
		VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
		VMD uses OpenGL to provide high performance 3-D molecular graphics and stereo viewing capabilities.
	www.dti3d.com /content/view/7/50 (368 words)

	Information about VMD at NERSC
		VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and scripting.
		VMD has a rich set of functionality for performing Visual Molecular Dynamics.
		VMD works well with projected display systems like the 3-D Projection Facility maintained by the Theoretical Biophysics Group.
	vis.lbl.gov /NERSC/Software/vmd (505 words)

	Seeing the Light
		Their work evolved into a program called Visual Molecular Dynamics (VMD), which enabled researchers to visualize large and complex biomolecular structures.
		VMD later became part of MDScope, a fully integrated program for computational molecular dynamics released by Schulten's group in 1995.
		A version of VMD for Windows was released in January 2000.
	access.ncsa.uiuc.edu /CoverStories/MolPhotodynamics/light3.html (389 words)

	CCL.NET 1999.04.05-006
		VMD "Visual Molecular Dynamics" 1.3 Announcement ------------------------------------------------ The Theoretical Biophysics group at the Beckman Institute For Advanced Science and Technology, the University of Illinois (U-C), is proud to announce the public release of VMD 1.3.
		VMD is a package for the visualization and analysis of biomolecular systems.
		VMD development is supported by the NIH National Center for Research Resources.
	www.ccl.net /cgi-bin/ccl/message.cgi?1999+04+05+006 (273 words)

	The Official MolScript Web Site: Other molecular graphics sites (Site not responding. Last check: 2007-10-28)
		Visual Molecular Dynamics (VMD), from the Theoretical Biophysics Group at the Beckman Institute, University of Illinois at Urbana-Champaign.
		SPOCK is a full-featured molecular graphics program developed by Jon A. Christopher while in the lab of Thomas O. Baldwin of the Department of Biochemistry and Biophysics at Texas A&M University.
		PREPI is a molecular graphics program which can be used to easily produce and interactively manipulate many different types of molecular representations (cartoons) as well as providing quantative information on secondary structural topology.
	www.avatar.se /molscript/other_molgraph.html (303 words)

	SAL- Other Scientific Fields - Chemistry, Biology & Related - VMD (Site not responding. Last check: 2007-10-28)
		VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed to be easy to use and modify.
		VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.
		It can also be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.
	sal.jyu.fi /Z/2/VMD.html (163 words)

	VMD Quick Help Summary
		VMD is one component of the MDScope software, which includes also the program NAMD (a portable, parallel molecular dynamics program) and the MDCOMM software to enable communication betweenVMD and NAMD.
		VMD understands commands which start with the following words; click on a command for a more complete synopsis.
		Several environment variables are used by VMD to determine the location of certain files and directories.
	bioweb.pasteur.fr /docs/doc-gensoft/vmd/vmd_help.html (1641 words)

	PhysOrgForum Science, Physics and Technology Discussion Forums -> help with peptide modelling
		RasMol and Chime: Molecular Visualization Freeware RasMol is a free program which displays molecular structure.
		VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics...
		II is a 3-D molecular modeling graphics program for the creation, modification, manipulation...
	forum.physorg.com /index.php?showtopic=1399 (590 words)

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